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nanocomp

Comparison of multiple long read datasets

https://github.com/wdecoster/nanocomp

Science Score: 26.0%

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    CITATION.cff file
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    DOI references
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    Scientific vocabulary similarity
    Low similarity (13.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Comparison of multiple long read datasets

Basic Info
  • Host: GitHub
  • Owner: wdecoster
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 302 KB
Statistics
  • Stars: 142
  • Watchers: 2
  • Forks: 9
  • Open Issues: 5
  • Releases: 1
Created almost 9 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.md

NanoComp

Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.

As of version 1.1.0 NanoComp will also create a static png image for dynamic html plots, as the latter can get quite big and slow to load for big datasets. This however requires that you install orca. Without orca the script still works, but no static copies of dynamic plots are created.

Twitter URL

INSTALLATION

pip install NanoComp
or
conda install bioconda::nanocomp

This script is written for Python3.

USAGE

``` NanoComp [-h] [-v] [-t THREADS] [-o OUTDIR] [-p PREFIX] [--verbose] [--raw] [--readtype {1D,2D,1D2}] [--barcoded] [--splitruns TSVFILE] [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}] [-n names [names ...]] [--plot {violin,box}] --title TITLE

General options: -h, --help show the help and exit -v, --version Print version and exit. -t, --threads THREADS Set the allowed number of threads to be used by the script -o, --outdir OUTDIR Specify directory in which output has to be created. -p, --prefix PREFIX Specify an optional prefix to be used for the output files. --verbose Write log messages also to terminal. --raw Store the extracted data in tab separated file.

Options for filtering or transforming input prior to plotting: --readtype {1D,2D,1D2} Which read type to extract information about from summary. Options are 1D, 2D, 1D2 --barcoded Barcoded experiment in summary format, splitting per barcode. --splitruns TSVFILE File: Split the summary on run IDs and use names in tsv file. Mandatory header fields are 'NAME' and 'RUN_ID'.

Options for customizing the plots created: -f, --format {'png'(default),'jpg','jpeg','webp','svg','pdf','eps','json'} Specify the output format of the plots. JSON output allows for customisation by the end-user after plotting the figures (https://plotly.com/python-api-reference/generated/plotly.io.read_json.html). -n, --names names Specify the names to be used for the datasets. -c, --colors colors Specify the colors to be used for the datasets. --plot {violin,box,ridge,false} Which plot type to use: 'box', 'violin' (default), 'ridge' (joyplot) or 'false' (no plots) --title TITLE Add a title to all plots, requires quoting if using spaces

Input data sources, one of these is required.: --fastq files [files ...] Data is in (compressed) fastq format. --fasta files [files ...] Data is in (compressed) fasta format. --summary files [files ...] Data is in (compressed) summary files generated by albacore or guppy. --bam files [files ...] Data is in sorted bam files.

```

Example file for --split_runs

EXAMPLES

NanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs NanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 run3 run4

EXAMPLE OUTPUT

loglength example box percentIdentity example

See more examples

I welcome all suggestions, bug reports, feature requests and contributions. Please leave an issue or open a pull request. I will usually respond within a day, or rarely within a few days.

CITATION

If you use this tool, please consider citing our publication.

Owner

  • Name: Wouter De Coster
  • Login: wdecoster
  • Kind: user
  • Location: Antwerp, Belgium
  • Company: VIB-UAntwerp

Bioinformatics postdoc using short and long read sequencing in neurodegenerative disorders at Rademakers Lab

GitHub Events

Total
  • Issues event: 14
  • Watch event: 37
  • Issue comment event: 14
  • Push event: 3
Last Year
  • Issues event: 14
  • Watch event: 37
  • Issue comment event: 14
  • Push event: 3

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 223
  • Total Committers: 4
  • Avg Commits per committer: 55.75
  • Development Distribution Score (DDS): 0.076
Past Year
  • Commits: 5
  • Committers: 1
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
wdecoster d****r@g****m 206
iliasbukraa i****a@g****m 14
Christian Brueffer c****n@b****o 2
ChristinaPapastolopoulou 6****u 1
Committer Domains (Top 20 + Academic)
brueffer.io: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 64
  • Total pull requests: 15
  • Average time to close issues: 4 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 51
  • Total pull request authors: 4
  • Average comments per issue: 3.92
  • Average comments per pull request: 0.33
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 0
  • Average time to close issues: about 6 hours
  • Average time to close pull requests: N/A
  • Issue authors: 5
  • Pull request authors: 0
  • Average comments per issue: 1.2
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • wdecoster (4)
  • callumparr (4)
  • schorlton (3)
  • devonorourke (3)
  • prasundutta87 (2)
  • HornDW (2)
  • aspitaleri (2)
  • adramir4 (1)
  • MariBGO (1)
  • albuskilili (1)
  • arz19893 (1)
  • Sophie-Gallina (1)
  • Annie-msi (1)
  • ggstatgen (1)
  • najohink (1)
Pull Request Authors
  • iliasbukraa (8)
  • wdecoster (4)
  • cbrueffer (2)
  • ChristinaPapastolopoulou (1)
Top Labels
Issue Labels
enhancement (8) question (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 238 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 77
  • Total maintainers: 1
pypi.org: nanocomp

Comparing runs of Oxford Nanopore sequencing data and alignments

  • Versions: 77
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 238 Last month
Rankings
Dependent packages count: 7.3%
Stargazers count: 7.9%
Downloads: 12.8%
Forks count: 13.3%
Average: 22.0%
Dependent repos count: 68.5%
Maintainers (1)
wdecoster
Last synced: 11 months ago

Dependencies

setup.py pypi
  • NanoPlot >=1.39.0
  • nanoget >=1.4.0
  • nanomath >=1.0.0
  • numpy >=1.16.5
  • pandas *
  • plotly >=3.4.2
  • psutil *
  • pyarrow *
.github/workflows/python-package-conda.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite